{"id":"W2162193618","doi":"10.2174/1875036200802010080","title":"Modeling Cooperative Gene Regulation Using Fast Orthogonal Search","year":2008,"lang":"en","type":"article","venue":"The Open Bioinformatics Journal","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":5,"is_retracted":false,"has_abstract":true,"ca_institutions":"Queen's University","funders":"Lawrence Berkeley National Laboratory","keywords":"Motif (music); Saccharomyces cerevisiae; Computer science; Computational biology; Transcription factor; Gene; Gene regulatory network; Biology; Gene expression; Genetics","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0006024635,0.000137313,0.0001351634,0.00003815603,0.0009185935,0.0002332622,0.0006036548,0.00008082409,0.00003554224],"category_scores_gemma":[0.00002225027,0.00009625642,0.00007021299,0.00009150241,0.00008641116,0.00003215484,0.0004048951,0.0002108045,0.00001245119],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00003924072,"about_ca_system_score_gemma":0.0003350198,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00001245857,"about_ca_topic_score_gemma":0.000007727573,"domain_scores_codex":[0.998968,0.00006171872,0.0004142085,0.00009618909,0.0002143408,0.0002455525],"domain_scores_gemma":[0.9992451,0.000006111962,0.0001373495,0.0002685661,0.0002499843,0.00009286268],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"simulation_or_modeling","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.00009167837,0.00003728462,0.0002166075,0.000008633969,0.0001110281,0.00000524297,0.001519782,0.8939167,0.102066,0.0002627033,0.0003117086,0.001452616],"study_design_scores_gemma":[0.000498647,0.00009520902,0.0001434984,0.00001427246,0.00001416359,0.002051901,0.0005963979,0.9881515,0.007958773,0.0001141126,0.0002033129,0.0001582496],"study_design_candidate":"simulation_or_modeling","study_design_consensus":"simulation_or_modeling","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.8396695,0.00007193952,0.1583192,0.00007355298,0.00009080705,0.0001883283,0.00001331339,0.000002588986,0.001570821],"genre_scores_gemma":[0.9573104,0.0003100572,0.04155969,0.0001983691,0.000223291,0.000002210934,0.00007038055,0.00001894894,0.0003066957],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.1176409,"threshold_uncertainty_score":0.7065172,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.04184068761405676,"score_gpt":0.2821583290921968,"score_spread":0.2403176414781401,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}